Different OLS regression procedures that lead to the same coefficients I've rewritten this question, because my phrasing and notation was confusing.
We're assuming OLS regression throughout this post.
If we have the data $\mathbf{y} \in \mathbb{R}^N$, $\mathbf{X}\in \mathbb{R}^{N \times M}$, and $\mathbf{Z} \in \mathbb{R}^{N \times L}$, then consider the following three different procedures to regress the data:

*

*Regress $\mathbf{X}$ on $\mathbf{Z}$ to get $\mathbf{X} = \mathbf{Z}\mathbf{\Gamma} + \mathbf{E}$. Define $\tilde{\mathbf{X}} \equiv \mathbf{E}$. Regress $\mathbf{y}$ on $\tilde{\mathbf{X}}$ to get $\mathbf{y} = \tilde{\mathbf{X}} \hat{\boldsymbol{\beta}}_1 + \boldsymbol{\epsilon}_1$.


*Concatenate the columns of $\mathbf{X}$ and $\mathbf{Z}$ to get a $N \times (M+L)$ matrix. Call this matrix $[\mathbf{X}\mathbf{Z}]$. Regress $\mathbf{y}$ on $[\mathbf{X}\mathbf{Z}]$ to get $\mathbf{y} = [\mathbf{X}\mathbf{Z}]\hat{\boldsymbol{\beta}}_{2,\text{total}} + \boldsymbol{\epsilon}_2$. Since we did column concatenation, we can write this as $\mathbf{y} = \mathbf{X} \hat{\boldsymbol{\beta}}_{2,\mathbf{X}} + \mathbf{Z} \hat{\boldsymbol{\beta}}_{2,\mathbf{Z}} + \boldsymbol{\epsilon}_2$.


*With $\tilde{\mathbf{X}}$ defined above, concatenate the columns of $\tilde{\mathbf{X}}$ and $\mathbf{Z}$ to get $[\tilde{\mathbf{X}} \mathbf{Z}]$. Regress $\mathbf{y}$ on $[\tilde{\mathbf{X}} \mathbf{Z}]$ to get $\mathbf{y} = [\tilde{\mathbf{X}} \mathbf{Z}] \hat{\boldsymbol{\beta}}_{3, \text{total}} + \boldsymbol{\epsilon}_3$. We can write this as $\mathbf{y} = \tilde{\mathbf{X}}\hat{\boldsymbol{\beta}}_{3,\tilde{\mathbf{X}}} + \mathbf{Z} \hat{\boldsymbol{\beta}}_{3,\mathbf{Z}} + \boldsymbol{\epsilon}_3$.
It turns out that:

*

*$\hat{\boldsymbol{\beta}}_1 = \hat{\boldsymbol{\beta}}_{2,\mathbf{X}} = \hat{\boldsymbol{\beta}}_{3, \tilde{\mathbf{X}}}$

*$\boldsymbol{\epsilon} _3 = \boldsymbol{\epsilon}_2 = \boldsymbol{\epsilon}_1 - \mathbf{Z}(\mathbf{Z}^\intercal \mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{y}$
I found these equalities by calculating the coefficients from the OLS regression coefficient formula $\hat{\boldsymbol{\beta}} = (\mathbf{X}^\intercal \mathbf{X})^{-1} \mathbf{X}^\intercal\mathbf{y}$ (assuming that $\mathbf{X}^\intercal\mathbf{X}$ is invertible), and I'll show the steps at the end--it's just some linear algebra stuff.
My question is: can we prove these equalities without taking pains to do the matrix algebra? In other words, although I know these equalities hold, I don't know why they hold. It might be worth noting that $\tilde{\mathbf{X}}$ is uncorrelated with $\mathbf{Z}$, but I'm not sure how to make a general argument around that.
----------------Below is the calculation----------------
Since the regressions are all OLS, we have:
$\mathbf{\Gamma} = (\mathbf{Z}^\intercal \mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{X}$,
$\hat{\boldsymbol{\beta}}_1 = (\tilde{\mathbf{X}}^\intercal \tilde{\mathbf{X}})^{-1}\tilde{\mathbf{X}}^\intercal\mathbf{y}$
$\hat{\boldsymbol{\beta}}_{2,\text{total}} = ([\mathbf{X}\mathbf{Z}]^\intercal[\mathbf{X}\mathbf{Z}])^{-1}[\mathbf{X}\mathbf{Z}]^\intercal\mathbf{y}$,
$\hat{\boldsymbol{\beta}}_{3,\text{total}} = ([\tilde{\mathbf{X}}\mathbf{Z}]^\intercal[\tilde{\mathbf{X}}\mathbf{Z}])^{-1}[\tilde{\mathbf{X}}\mathbf{Z}]^\intercal\mathbf{y}$.
We may express $\hat{\boldsymbol{\beta}}_1$, $\hat{\boldsymbol{\beta}}_{2,\text{total}}$, and $\hat{\boldsymbol{\beta}}_{3,\text{total}}$ in terms of $\mathbf{X}$, $\mathbf{y}$, and $\mathbf{Z}$ for the sake of comparison.
First, let's calculate $\hat{\boldsymbol{\beta}}_1$.
Plug in $\mathbf{\Gamma}$ to the definition of $\tilde{\mathbf{X}}$, we get $\tilde{\mathbf{X}} \equiv \mathbf{E} = \mathbf{X} - \mathbf{Z}\mathbf{\Gamma} = \mathbf{X} - \mathbf{Z} (\mathbf{Z}^\intercal \mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{X}$.
To keep the equations compact, define $\mathbf{S} \equiv \mathbf{Z} (\mathbf{Z}^\intercal \mathbf{Z})^{-1}\mathbf{Z}^\intercal$. So, $\tilde{\mathbf{X}} = (\mathbf{I} - \mathbf{S})\mathbf{X}$.
Note the following properties of $\mathbf{S}$:

*

*$\mathbf{S}^\intercal = \mathbf{S}$


*$(\mathbf{I}-\mathbf{S})^\intercal = \mathbf{I}-\mathbf{S}$


*$\mathbf{S} \mathbf{S} = \mathbf{S}$


*$(\mathbf{I}-\mathbf{S})(\mathbf{I}-\mathbf{S}) = \mathbf{I}-\mathbf{S}$


*$\mathbf{S}(\mathbf{I}-\mathbf{S}) = (\mathbf{I}-\mathbf{S})\mathbf{S} = 0$
Now, plug in $\tilde{\mathbf{X}}$ to the equation for $\hat{\boldsymbol{\beta}}_1$, we get:
$$\begin{align}\hat{\boldsymbol{\beta}}_1 &= (\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})^\intercal (\mathbf{I} - \mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})^\intercal\mathbf{y} \\ &=(\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})\mathbf{y}\end{align}$$
To calculate $\hat{\boldsymbol{\beta}}_{2,\text{total}}$, we use the following equation:
$\begin{align}\begin{bmatrix}\mathbf{A} & \mathbf{B} \\ \mathbf{C} & \mathbf{D}\end{bmatrix}^{-1}=\begin{bmatrix}\mathbf{P} & -\mathbf{P} \mathbf{B} \mathbf{D}^{-1}\\-\mathbf{D}^{-1}\mathbf{C}\mathbf{P} & \mathbf{D}^{-1}+\mathbf{D}^{-1}\mathbf{C}\mathbf{P}\mathbf{B}\mathbf{D}^{-1}\end{bmatrix}\end{align}$
where $\mathbf{P} = (\mathbf{A} - \mathbf{B} \mathbf{D}^{-1}\mathbf{C})^{-1}$, assuming $\mathbf{D}$ invertible.
With this equation, we can expand $([\mathbf{X}\mathbf{Z}]^\intercal[\mathbf{X}\mathbf{Z}])^{-1}$ in the equation for $\hat{\boldsymbol{\beta}}_{2,\text{total}}$.
Since $([\mathbf{X}\mathbf{Z}]^\intercal[\mathbf{X}\mathbf{Z}])^{-1} = \begin{bmatrix}\mathbf{X}^\intercal\mathbf{X} & \mathbf{X}^\intercal\mathbf{Z} \\ \mathbf{Z}^\intercal \mathbf{X} & \mathbf{Z}^\intercal \mathbf{Z}\end{bmatrix}^{-1}$, let $\mathbf{A} = \mathbf{X}^\intercal\mathbf{X}$, $\mathbf{B} = \mathbf{X}^\intercal\mathbf{Z}$, $\mathbf{C} = \mathbf{Z}^\intercal \mathbf{X}$, and $\mathbf{D} = \mathbf{Z}^\intercal\mathbf{Z}$.
So, $\mathbf{P} = (\mathbf{X}^\intercal\mathbf{X}-\mathbf{X}^\intercal\mathbf{Z}(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{X})^{-1} = (\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}$.
As mentioned in the description of the procedure, we can write $\hat{\boldsymbol{\beta}}_{2,\text{total}}$ as the row concatenation of $\hat{\boldsymbol{\beta}}_{2,\mathbf{X}}$ and $\hat{\boldsymbol{\beta}}_{2,\mathbf{Z}}$. We calculate them separately here.
$$\begin{align}\hat{\boldsymbol{\beta}}_{2,\mathbf{X}} &= \mathbf{P}\mathbf{X}^\intercal\mathbf{y} - \mathbf{P}\mathbf{B}\mathbf{D}^{-1}\mathbf{Z}^\intercal\mathbf{y}\\&=(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal\mathbf{y} - (\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal\mathbf{Z}(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{y}\\&=(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y}\end{align}$$
$$\begin{align}\hat{\boldsymbol{\beta}}_{2,\mathbf{Z}} &= -\mathbf{D}^{-1}\mathbf{C}\mathbf{P}\mathbf{X}^\intercal\mathbf{y} + (\mathbf{D}^{-1}+\mathbf{D}^{-1}\mathbf{C}\mathbf{P}\mathbf{B}\mathbf{D}^{-1})\mathbf{Z}^\intercal\mathbf{y}\\&=-(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal\mathbf{y} + (\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{y} + (\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal\mathbf{Z}(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{y}\\&=-(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y}+(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{y}\end{align}$$
To calculate $\hat{\boldsymbol{\beta}}_{3,\text{total}}$, we again calculate $\hat{\boldsymbol{\beta}}_{3,\tilde{\mathbf{X}}}$ and $\hat{\boldsymbol{\beta}}_{3,\mathbf{Z}}$ separately.
But, to do this, note that we only need to substitute every $\mathbf{X}$ in $\hat{\boldsymbol{\beta}}_{2,\mathbf{X}}$ and $\hat{\boldsymbol{\beta}}_{2,\mathbf{Z}}$ with $\tilde{\mathbf{X}}$.
$$\begin{align}\hat{\boldsymbol{\beta}}_{3,\tilde{\mathbf{X}}} &= (\tilde{\mathbf{X}}^\intercal(\mathbf{I}-\mathbf{S})\tilde{\mathbf{X}})^{-1}\tilde{\mathbf{X}}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y} \\ &= (\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})^\intercal(\mathbf{I}-\mathbf{S})(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y} \\ &=  (\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y}\end{align}$$
We're not going to explicitly do the substitution for $\hat{\boldsymbol{\beta}}_{3,\mathbf{Z}}$, and the reason will be clear as we compare the $\boldsymbol{\epsilon}$'s.
So far, we have demonstrated that $\hat{\boldsymbol{\beta}}_1 = \hat{\boldsymbol{\beta}}_{2,\mathbf{X}} = \hat{\boldsymbol{\beta}}_{3, \tilde{\mathbf{X}}}=(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y}$. We can now demonstrate the relation between $\boldsymbol{\epsilon}_1$, $\boldsymbol{\epsilon}_2$, and $\boldsymbol{\epsilon}_3$.
We directly calculate $\boldsymbol{\epsilon}_1$ and $\boldsymbol{\epsilon}_2$ as follows.
$$\begin{align}\boldsymbol{\epsilon}_1 &= \mathbf{y} - \tilde{\mathbf{X}}\hat{\boldsymbol{\beta}}_1 \\ &= \mathbf{y} - (\mathbf{I}-\mathbf{S})\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})\mathbf{y}\end{align}$$
$$\begin{align}\boldsymbol{\epsilon}_2 &= \mathbf{y} - \mathbf{X} \hat{\boldsymbol{\beta}}_{2,\mathbf{X}} - \mathbf{Z} \hat{\boldsymbol{\beta}}_{2,\mathbf{Z}} \\ &= \mathbf{y} -\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y} - \mathbf{Z}\left\{-(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y}+(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{y}\right\} \\ &= \mathbf{y} -\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y} + \mathbf{S}\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y} - \mathbf{S}\mathbf{y} \\ &= \mathbf{y} - (\mathbf{I}-\mathbf{S})\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I} - \mathbf{S})\mathbf{y} - \mathbf{S}\mathbf{y} \end{align}$$
Indeed, $\boldsymbol{\epsilon}_2 = \boldsymbol{\epsilon}_1 -\mathbf{S}\mathbf{y}$.
To calculate $\boldsymbol{\epsilon}_3$, we first examine the term $\mathbf{Z} \hat{\boldsymbol{\beta}}_{3,\mathbf{Z}}$. Remember that we substitute $\mathbf{X}$ in $\hat{\boldsymbol{\beta}}_{2,\mathbf{Z}}$ with $\tilde{\mathbf{X}}$ to get $\hat{\boldsymbol{\beta}}_{3,\mathbf{Z}}$. So,
$\begin{align}\mathbf{Z} \hat{\boldsymbol{\beta}}_{3,\mathbf{Z}} &= -\mathbf{Z}(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\tilde{\mathbf{X}}(\tilde{\mathbf{X}}^\intercal(\mathbf{I}-\mathbf{S})\tilde{\mathbf{X}})^{-1}\tilde{\mathbf{X}}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y}+\mathbf{Z}(\mathbf{Z}^\intercal\mathbf{Z})^{-1}\mathbf{Z}^\intercal\mathbf{y}\\ &= -\mathbf{S}\tilde{\mathbf{X}}(\tilde{\mathbf{X}}^\intercal(\mathbf{I}-\mathbf{S})\tilde{\mathbf{X}})^{-1}\tilde{\mathbf{X}}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y}+\mathbf{S}\mathbf{y}\end{align}$
But $\mathbf{S}\tilde{\mathbf{X}} = \mathbf{S}(\mathbf{I}-\mathbf{S})\mathbf{X} = 0$ by the fifth property of $\mathbf{S}$. Therefore, $\mathbf{Z} \hat{\boldsymbol{\beta}}_{3,\mathbf{Z}} = \mathbf{S}\mathbf{y}$, and
$$\begin{align}\boldsymbol{\epsilon}_3 &= \mathbf{y} - \tilde{\mathbf{X}}\hat{\boldsymbol{\beta}}_{3,\tilde{\mathbf{X}}} - \mathbf{Z} \hat{\boldsymbol{\beta}}_{3,\mathbf{Z}} \\ &= \mathbf{y} - (\mathbf{I}-\mathbf{S})\mathbf{X}(\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{X})^{-1}\mathbf{X}^\intercal(\mathbf{I}-\mathbf{S})\mathbf{y} - \mathbf{S}\mathbf{y}\end{align}$$
Thus, $\boldsymbol{\epsilon}_3=\boldsymbol{\epsilon}_2=\boldsymbol{\epsilon}_1-\mathbf{S}\mathbf{y}$.
 A: @Sextus Empiricus gives a geometric perspective, while @J. Delaney gives a clever reparameterization. Let me provide an alternative algebraic perspective that appeals to the first order condition of OLS, but avoids tedious matrix computations. Throughout, I will let $\mathbf Y \in \mathbb R^{n\times 1}$ be the column matrix of outcomes and $\mathbf X = \mathbb R^{n\times k}$ be the design matrix such that each row is the values of $\mathbf x$ for a single observation. Let $\beta \in \mathbb R^{k\times 1}$ be the vector of parameters. Also, throughout, I will adopt the econometrician's convention of taking $'$ to mean transpose.
Recall that the OLS estimator is obtained by solving the following minimization problem:
$$\hat\beta^{OLS} = \mathrm{argmin}_\beta\, (\mathbf Y - \mathbf X\beta)'(\mathbf Y-\mathbf X\beta)$$
Since this is a strictly convex objective in $\beta$, it suffices to take a first order condition (FOC). Differentiating with respect to $\beta$, the FOC can be rearranged to state that
$$\mathbf X'(\mathbf Y - \mathbf X\beta) = 0$$
Consider now, the partition of $\mathbf X = [\mathbf X_1\ \mathbf X_2]$ where $\mathbf X_1\in\mathbb R^{n\times k_1}$, $\mathbf X_2\in\mathbb R^{n\times k_2}$ with $k_1 + k_2 = k$. Similarly, partition $\beta = [\beta_1'\,\beta_2']'$, so that $\mathbf X\beta = X_1\beta_1 + X_2\beta_2$. In that case, we can split the OLS FOC into the two sets of FOCs :
$$\mathbf X_1'(\mathbf Y - \mathbf X_1\beta_1 - \mathbf X_2\beta_2) = 0$$
$$\mathbf X_2'(\mathbf Y - \mathbf X_1\beta_1 - \mathbf X_2\beta_2) = 0$$
Let us now rearrange the second set of FOCs to solve for $\beta_2$ in terms of everything else:
$$\hat\beta_2^{OLS} = (\mathbf X_2'\mathbf X_2)^{-1}\mathbf X_2'(\mathbf Y - \mathbf X_1\beta_1)$$
We can now plug this expression for $\beta_2$ back into the first set of FOCs to attain
$$0 = \mathbf X_1'[\mathbf Y - \mathbf X_1\beta_1 -\mathbf X_2(\mathbf X_2\mathbf X_2)^{-1}\mathbf X_2'(\mathbf Y-\mathbf X_1'\beta_1)]$$
Grouping together the terms involving $\mathbf Y$ and the terms involving $\mathbf X_1\beta_1$, we get
$$0 = \mathbf X_1'[(\mathbf I - \mathbf X_2(\mathbf X_2\mathbf X_2)^{-1}\mathbf X_2') \mathbf Y + (\mathbf I - \mathbf X_2(\mathbf X_2\mathbf X_2)^{-1}\mathbf X_2')\mathbf X_1\beta_1]$$
But now, note that $\mathbf M_2 = \mathbf I - \mathbf X_2'(\mathbf X_2\mathbf X_2)^{-1}\mathbf X_2$ is the so-called annialator matrix for $\mathbf X_2$, in the sense that for any vector $\mathbf A\in\mathbb R^{n\times 1}$, $\mathbf M_2 \mathbf A$ can be interpreted as the residuals from the OLS regression of $\mathbf A$ on $\mathbf X_2$. We can solve the FOC above to obtain:
$$\hat\beta_1^{OLS} = (\mathbf X_1'\mathbf M_2\mathbf X_1)^{-1}(\mathbf X_1' \mathbf M_2 \mathbf Y)$$
Noting that $\mathbf M_2$ is symmetric ($\mathbf M_2'=\mathbf M_2$) and idempotent ($\mathbf M_2 \mathbf M_2 = \mathbf M_2$), this final expression can, given all of the above, be reinterpreted as the regression of the $\mathbf Y$ residuals on the $\mathbf X_1$ residuals, as stated in your question.
A: When you have a linear regression of the form
$$ y = X\beta_1 + Z\beta_2 + \varepsilon$$
and $X^TZ = 0$ , then it is equivalent to independently regressing $y$ on $X$ and $Z$. This is easy to see because the matrix
$$([XZ]^T[XZ])^{-1} = \begin{pmatrix} X^TX & 0 \\ 0 & Z^TZ\end{pmatrix}^{-1} = \begin{pmatrix} (X^TX)^{-1} & 0 \\ 0 & (Z^TZ)^{-1}\end{pmatrix}$$
is block diagonal, it's inverse is therefore also block diagonal and we get $\beta_1 = (X^T X)^{-1} X^Ty$ and $\beta_2 = (Z^T Z)^{-1} Z^Ty$.
Now notice that by your construction $Z^T \tilde X = 0$
($Z^T\tilde X = Z^T(X - Z\hat\Gamma) = Z^T X - Z^T Z (Z^T Z)^{-1}Z^TX = Z^T X - Z^T X = 0)$
so the coefficient $\beta_1$ of the regression $y = \tilde X \beta_1$ is the same as in the regression  $y = \tilde X \beta_1 + Z\beta_2$, which explains the equivalence of (1) and (3).
In case (2) we can re-parametrize the second coefficient: $y = X\beta_1 + Z\beta_2 = (X-Z\hat\Gamma)\beta_1 + Z(\beta_2 +\hat\Gamma \beta_1) \equiv \tilde X\beta_1 + Z\beta_3$, which brings this to a similar form, so $\beta_1$ here is also equivalent to the two other cases.
A: Below is a geometric viewpoint similar to an answer to a different question: Intuition behind $(X^TX)^{-1}$ in closed form of w in Linear Regression

The regression is a perpendicular projection onto the vectors in the columns of $X$ and $Z$. What you are basically doing is defining a different vector $\bar{X}$ such that the coordinates associated with the projection remain the same.
This alternative vector is drawn in the image with a red on the right side.
The vector $\bar{X}$ is perpendicular to $Z$ and that is why all those coefficients $\beta$ turn out to be the same.
If $Z$ and $\bar{X}$ are perpendicular then

*

*The regression $$Y \sim \beta_1 \bar{X} + \beta_2 Z$$ and  $$Y \sim \beta_1^\prime \bar{X} $$ will be the same in the sense $\beta_1 = \beta_1^\prime$


*The regression  $$Y \sim \beta_1 \bar{X} + \beta_2 Z$$ and  $$Y \sim \beta_1^{\prime\prime} (\bar{X} + a Z) + \beta_2 Z$$ with $a$ some constant, will be the same in the sense $\beta_1 = \beta_1^{\prime\prime}$.
Note that we can write $X = \bar{X} + a Z$. The difference between $X$ and $\bar{X}$ is some multiple of $Z$.
